Related ArticlesTheory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data.
J Biomol NMR. 1995 Apr;5(3):245-58
Authors: Chylla RA, Markley JL
A general theory has been developed for the application of the maximum likelihood (ML) principle to the estimation of NMR parameters (frequency and amplitudes) from multidimensional time-domain NMR data. A computer program (ChiFit) has been written that carries out ML parameter estimation in the D-1 indirectly detected dimensions of a D-dimensional NMR data set. The performance of this algorithm has been tested with experimental three-dimensional (HNCO) and four-dimensional (HN(CO)-CAHA) data from a small protein labeled with 13C and 15N. These data sets, with different levels of digital resolution, were processed using ChiFit for ML analysis and employing conventional Fourier transform methods with prior extrapolation of the time-domain dimensions by linear prediction. Comparison of the results indicates that the ML approach provides superior frequency resolution compared to conventional methods, particularly under conditions of limited digital resolution in the time-domain input data, as is characteristic of D-dimensional NMR data of biomolecules. Close correspondence is demonstrated between the results of analyzing multidimensional time-domain NMR data by Fourier transformation, Bayesian probability theory [Chylla, R.A. and Markley, J.L. (1993) J. Biomol. NMR, 3, 515-533], and the ML principle.
[NMRpipe Yahoo group] How to collapse multiplets into singlets by Maximum entropy algorith
How to collapse multiplets into singlets by Maximum entropy algorith
Hi, Recently, I ran a 3D HCC-TOCSY experiment on a uniformly 13C labeled sample. Therefore, all peaks are split due to carbon-carbon coupling. The paper
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02-15-2012 03:40 AM
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 30 December 2011</br>
Claudio*Luchinat, Malini*Nagulapalli, Giacomo*Parigi, Luca*Sgheri</br>
Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively...
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12-31-2011 10:40 AM
[Question from NMRWiki Q&A forum] shake routine and ncon parameter
shake routine and ncon parameter
Trying to do molecular dynamics with explicit water molecules I came across a problem with SHAKE routine:
shake reference = parameters bonds (hydrogen) (all) tolerance = 1.0e-06 nconstraints=8000end
and error message after this is:
X-PLOR>shake SHAKE> reference = parameters SHAKE> bonds (hydrogen) (all) SELRPN: 7142 atoms have been selected out of 11032 SELRPN: 11032 atoms have been selected out of 11032 SHKSET: reference = parameters %XREFIN-ERR: allocation for SHAKE-constraints exceeded ...
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10-27-2011 11:42 PM
[Question from NMRWiki Q&A forum] Bruker GRPDLY Parameter
Bruker GRPDLY Parameter
I am new to working with Bruker-style NMR data and am experiencing confusion with regard to Bruker's digital filtering. Some experiments on our Bruker spectrometers result in valid decim/dspfvs/grpdly values in the acqus output file, but other spectrometers give a value of -1 for grpdly. Does anyone know what this value means? More importantly, how can I calculate how many points to left-shift the Bruker fid for offline processing when grpdly does not contain the value?
Thank you.
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nmrlearner
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11-11-2010 04:33 PM
Chemical shift tensors: Theory and application to molecular structural problems
Chemical shift tensors: Theory and application to molecular structural problems
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 22 October 2010</br>
Julio C., Facelli</br>
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10-23-2010 07:42 AM
Automatic maximum entropy spectral reconstruction in NMR
Automatic maximum entropy spectral reconstruction in NMR
Mehdi Mobli, Mark W. Maciejewski, Michael R. Gryk and Jeffrey C. Hoch
Journal of Biomolecular NMR; 2007; 39(2) pp 133 - 139
Abstract:
Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time...
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08-05-2008 01:24 PM
Refinement against order parameter with XPLOR
New 2.10 release of XPLOR-NIH can now do a refinement against order parameters. You can get an idea what this refinement can be used for from the this paper.
Info about new features of XPLOR-NIH 2.10 from XPLOR-NIH website: - new parameter/topology file naming convention: NMR protein refinement should now use topology file protein.top and parameter file protein.par.
- new command: tclXplor which calls xplor -tcl. Can be used as command interpreter
- new potential term OrderPot to enable refinement against order parameters.
- update to PrePot from Junji Iwahara
- CSAPot: 15N CSAs...
Theory and application of the maximum likelihood principle to NMR parameter estimatio
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